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<h1>MarvinSketch: parameters and events</h1>
<h3 align=center>Version 5.3.1</h3>

<h2>Contents</h2>

<ol>

<li><a HREF="#parameters">Parameters</a>
 	<ol>
    <li><a HREF="#appletandbeans">Applet and JavaBeans parameters</a></li>
	<ol>
	<li><a HREF="#displayparameters">Display parameters</a></li>
	<li><a HREF="#structuredisplayparameters">Structure display parameters</a></li>
	<li><a HREF="#structureparameters">Structure parameters</a></li>
	<li><a HREF="#otherparameters">Other parameters</a></li>
	</ol>    
<!--APPLETONLY_BEGIN-->
    <li><a HREF="#appletonly">Applet only parameters</a></li>
<!--APPLETONLY_END-->
	</ol>
</li>

</ol>

<center><div class="lenia">&nbsp;</div></center>
<h2><a class="anchor" name="parameters">1 &nbsp; Parameters</a></h2>
<h3><a class="anchor" name="appletandbeans">1.1 &nbsp; Applet and JavaBeans parameters</a></h3>
Parameters of the <em>MSketch</em> and <em>JMSketch</em> applets can be set using
the <code>&lt;param&gt;</code> HTML tag.

<p>
<h4><a class="anchor" name="displayparameters">1.1.1 &nbsp; Display parameters</a></h4>

<blockquote>
<table BORDER=0 cellpadding="4" cellspacing="0" class="colored-grid" width="800">
<tr align="CENTER"><th width="20%">Parameter</th><th>Meaning</th><th width="10%">Default</th></tr>

<tr valign="TOP"><td><a class="text" name="parameters.addRemoveHatomsEnabled"><code>addRemoveHatomsEnabled</code></a></td>
    <td><b>Add/Remove Explicit Hydrogens</b> is enabled or disabled
    in the <b>Structure</b> menu. It will be disabled if this parameter is
    false.</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomStrings"><code>atomStrings</code></a></td>
    <td>Comma-separated list of string type
	atom properties to be enabled.
	<ul>
	<li><code>alias</code> - atom aliases</li>
	<li><code>pseudo</code> - pseudoatoms</li>
	<li><code>smarts</code> - SMARTS query atom string</li>
        <li><code>value</code> - atom values</li>
        </ul>
	Example: <code>&quot;smarts&quot;</code>.
	</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.autoscale"><code>autoscale</code></a></td>
    <td>How to display a loaded molecule:
	<ul>
	<li><code>&quot;true&quot;</code> - fit to the applet's window</li>
	<li><code>&quot;false&quot;</code> - use default scaling</li>
	</ul>
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.background"><code><strike>background</strike></code></a></td>
    <td>Deprecated.</td>
    <td>&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.bondDraggedAlong"><code>bondDraggedAlong</code></a></td>
    <td>Bond in hand is visible
	(<code>true</code>) or not (<code>false</code>).
	This option can also be set on the
	<strong>Edit</strong>/<strong>Preferences</strong>/<strong>MarvinSketch</strong> panel.
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr VALIGN=TOP><td><a class="text" name="parameters.customizationEnabled"><code>customizationEnabled</code></a></td>
    <td>Specifies whether an end-user can customize the user interface.
    Setting this parameter to <code>false</code> disables the View/Customize dialog
    and the View/Configurations menu.
    </td>
    <td ALIGN=CENTER><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.dispQuality"><code>dispQuality</code></a></td>
    <td>Display quality.
	<ul>
	<li><code>0</code> - low quality, faster rendering</li>
	<li><code>1</code> - high quality (antialiasing), slower rendering</li>
	</ul>
	</td>
    <td align="CENTER"><code>1</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.elements"><code>elements</code></a></td>
    <td>Comma-separated list of allowed
	elements (<code>H</code>, <code>He</code>, <code>Li</code>, ...).
	All elements in an atomic number interval can be
	specified with the short <code>X-Y</code> notation.<br>
	Example: <code>&quot;B-F,P-Cl&quot;</code>.
	Here <code>B-F</code> is equivalent to <code>B,C,N,O,F</code>.<br>
	</td>
    <td align="CENTER"><code>H-Ha</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.extraBonds"><code>extraBonds</code></a></td>
    <td>Comma-separated list of extra bond
	types.
	<ul>
	<li><code>arom</code> - Aromatic bond</li>
	<li><code>any</code> - Any bond</li>
	<li><code>1or2</code> - &quot;Single or Double&quot; query bond</li>
	<li><code>aromany</code> - &quot;Single or Aromatic&quot; and
		&quot;Double or Aromatic&quot; query bond types</li>
	<li><code>topology</code> - &quot;Chain&quot; and &quot;Ring&quot; bonds
	    (in molfiles)</li>
	<li><code>wedge</code> - Up and Down stereo wedge bonds</li>
	<li><code>either</code> - &quot;Up or Down&quot; and
	    &quot;Cis or Trans&quot;</li>
	<li><code>ctu</code> - &quot;Cis or Unspecified&quot; and
	    &quot;Trans or Unspecified&quot;</li>
        <li><code>coordinate</code> - Coordinate bond</li>
        </ul>
	Example: <code>&quot;arom,wedge&quot;</code>.<br>
	See also: <a HREF="queryprops.html">Query properties in file formats.</a>
	</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.molbg"><code>molbg</code></a></td>
    <td>Molecule background color in hexadecimal value.
    Sets the background color of the molecule canvas.</td>
    <td>#ffffff</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.moreEnabled"><code>moreEnabled</code></a></td>
    <td>Enable/disable the Periodic System also called <strong>More</strong>
	button.</td>
    <td align="CENTER"><code>true</code></td></tr>
    <tr valign="TOP"><td><a class="text" name="parameters.queryAtoms"><code>queryAtoms</code></a></td>
    <td>Comma-separated list of query atoms
	and properties.
	<ul>
	<li><code>any</code> - any atom
	    (&quot;A&quot; in molfile, &quot;*&quot; in SMARTS),</li>
	<li><code>arom</code> - aliphatic and aromatic, (&quot;a&quot; and &quot;A&quot; in SMARTS),</li>
	<li><code>conn</code> - total number of connections, (&quot;X&quot; in SMARTS),</li>
	<li><code>H</code> - total number of hydrogens, (&quot;H&quot; in SMARTS),</li>
	<li><code>hetero</code> - heteroatom
	    (&quot;Q&quot; in molfile, &quot;[!C!H]&quot; in SMARTS),</li>
	<li><code>list</code> - atom list,</li>
	<li><code>notlist</code> - atom 'NOT' list,</li>
	<li><code>Rgroup</code> - Rgroups,</li>
	<li><code>rings</code> - &quot;R&quot; in SMARTS,</li>
	<li><code>srs</code> - smallest ring size, &quot;r&quot; in SMARTS,</li>
	<li><code>val</code> - valence, &quot;v&quot; in SMARTS,</li>
	</ul>
	Example: <code>&quot;list,notlist&quot;</code>.<br>
	See also: <a HREF="queryprops.html">Query properties in file formats.</a>
	</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.reactionSupport"><code>reactionSupport</code></a></td>
    <td>Enables/disables reaction arrow drawing.
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.simpView"
    ><a class="text" name="simpView"><code>simpView</code></a></a></td>
    <td>Visibility of the currently used bond at the mouse cursor.</td>
    <td>&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchArrowHeadLength"
    ><a class="text" name="sketchArrowHeadLength"><code>sketchArrowHeadLength</code></a></a></td>
    <td>Length of the displayed arrow head in Angstroms. It only affects graphical arrows.</td>
    <td><code>0.8</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchArrowHeadWidth"
    ><a class="text" name="sketchArrowHeadWidth"><code>sketchArrowHeadWidth</code></a></a></td>
    <td>Width of the displayed arrow head in Angstroms. It only affects graphical arrows.</td>
    <td><code>0.5</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchArrowTailLength"
    ><a class="text" name="sketchArrowTailLength"><code>sketchArrowTailLength</code></a></a></td>
    <td>Length of the displayed arrow tail in Angstroms. It only affects graphical arrows.</td>
    <td><code>0.8</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchArrowTailWidth"
    ><a class="text" name="sketchArrowTailWidth"><code>sketchArrowTailWidth</code></a></a></td>
    <td>Width of the displayed arrow tail in Angstroms. It only affects graphical arrows.</td>
    <td><code>0.5</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.statusBar"><code>statusBar</code></a></td>
    <td>Enable the status bar.</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.tmpls"><code>tmpls0</code></a><br><code>tmpls1</code><br><code>tmpls2</code><br>...
	</td>
    <td>The format of this parameter is
	:<i>name</i>:<i>file</i>, where
	<i>name</i> is the template set name, <i>file</i> is the
	sdf or cssdf file containing the template structures.
        <br>
	The file can be optionally compressed with GZIP (Java &gt;= 1.1).
	A template molecule is automatically converted to 2D if the
	<i>mol2dcmd</i> field contains one of the following values:
	<ul>
	<li><code>z=0</code> - for trivial conversion,</li>
	<li><code>clean</code> - for sophisticated 2D cleaning.</li>
	</ul>
	For automatic 3D conversion, the value of the <i>mol3dcmd</i> field
	must be
	<ul>
	<li><code>clean</code> - for sophisticated 3D cleaning.</li>
	</ul>
	Templates may have abbreviations if the <i>abbreviation</i> fields
	are specified.

	</td>
    <td align="CENTER">
	<a HREF="templates.html#default"><em>click here</em></a>
	</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.ttmpls"><code>ttmpls0</code></a><br><code>ttmpls1</code><br><code>ttmpls2</code><br>...
	</td>
    <td>Templates to be displayed on the template toolbar.
	Same as <a HREF="#parameters.tmpls">tmpls</a> but these template
	groups will also appear on the template toolbar by default.</td>
    <td align="CENTER">
	<a HREF="templates.html#default"><em>click here</em></a>
	</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.template.2d"><code>template.2d</code></a>
	</td>
    <td>Enables (true) or disables (false) to change the visible template groups
        on the <a href="../sketch/gui/toolbars.html#templates">Advanced Templates Toolbar</a>.<br>
        When enabled, the visibility of all template groups can be altered using the Template Library.</td>
    <td align="CENTER">
	true
	</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.templateToolbarCustomizable"><code>templateToolbarCustomizable</code></a>
	</td>
    <td>Enables (true) or disables (false) to change the visible template groups
        on the <a href="../sketch/gui/toolbars.html#templates">Advanced Templates Toolbar</a>.<br>
        When enabled, the visibility of all template groups can be altered using the Template Library.</td>
    <td align="CENTER">
	true
	</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.transferButtonIcon"><code>transferButtonIcon</code></a></td>
    <td>Sets the location of a custom icon for the Transfer action.</td>
    <td>&nbsp</td>
</tr>
<tr valign="TOP"><td><a class="text" name="parameters.transferButtonText"><code>transferButtonText</code></a></td>
    <td>Sets custom text for the Transfer action.</td>
    <td>&nbsp</td>
</tr>
<tr valign="TOP"><td><a class="text" name="parameters.transferButtonVisible"><code>transferButtonVisible</code></a></td>
    <td>Makes the Transfer button visible on the General Toolbar.</td>
    <td align="center"><code>false</code></td>
</tr>
<tr valign="TOP"><td><a class="text" name="parameters.viewonly"><code>viewonly</code></a></td>
    <td>Visualization mode:
	hide editing buttons;
	<code>&quot;true&quot;</code> or <code>&quot;false&quot;</code>.
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.verticalbar"><code><strike>verticalbar</strike></code></a></td>
    <td>Deprecated.</td>
    <td align="CENTER"><code>&nbsp;</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.xtmpls"><code>xtmpls</code></a></td>
    <td>File containing extra templates.
	Extra templates are placed beside the normal templates and they appear on
        the template toolbar by default.
        (see <a HREF="#parameters.tmpls">tmpls</a>).
	</td>
    <td align="LEFT">&nbsp;</td>
    </tr>
<tr valign="TOP"><td><a class="text" name="parameters.2dviewerEnabled"><code>2dviewerEnabled</code></a></td>
    <td>Enable (true) or disable(false) 2D viewer
    </td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.3dviewerEnabled"><code>3dviewerEnabled</code></a></td>
    <td>Enable (true) or disable(false) 3D viewer
    </td>
    <td align="CENTER"><code>true</code></td></tr>
</table>
</blockquote>

<h4><a class="anchor" name="structuredisplayparameters">1.1.2 &nbsp; Structure display parameters</a></h4>
<blockquote>
<table BORDER=0 cellpadding="4" cellspacing="0" class="colored-grid" width="800">
<tr align="CENTER"><th width="20%">Parameter</th><th>Meaning</th><th width="10%">Default</th></tr>
<tr valign="TOP"><td><a class="text" name="parameters.absLabel"
    ><a class="text" name="absLabel"><code>absLabel</code></a></a></td>
    <td>Show (true) or hide (false) "Absolute" label</td>
    <td>&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomFont"><code>atomFont</code></a></td>
    <td>Atom symbol/label font:
	<code>Serif</code>, <code>SansSerif</code> or <code>Monospaced</code>
	</td>
    <td align="CENTER"><code>SansSerif</code></td></tr>
<!--<tr valign="TOP"><td><a class="text" name="parameters.labels"><code>labels</code></a></td>
    <td>Show (true) or hide (false) atom labels
	</td>
    <td align="CENTER"><code>true</code></td></tr>-->
<tr valign="TOP"><td><a class="text" name="parameters.atomMappingVisible"><code>atomMappingVisible</code></a></td>
    <td>Show (true) or hide (false) atom mapping
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomNumbersVisible"><code>atomNumbersVisible</code></a></td>
    <td>Show (true) or hide (false) atom numbers
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomsize"><code>atomsize</code></a></td>
    <td>Atom symbol font size
	in C-C bond length units:<br>
	<center>
	<em>atomsize</em>*1.54 &Aring; = <em>atomsize</em>*<em>scale</em> points
	</center>
	</td>
    <td align="CENTER"><code>0.4</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomSymbolsVisible"><code>atomSymbolsVisible</code></a></td>
    <td>Show (true) or hide (false) atom symbols
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="3d.ballRadius"><code>ballRadius</code></a></td>
    <td>Ball radius for
	&quot;ballstick&quot; <a HREF="#3d.rendering">rendering mode</a>,
	in units of covalent radius.</td>
    <td align="CENTER"><code>0.5</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.bondLengthVisible"><code>bondLengthVisible</code></a></td>
    <td>Show (true) or hide (false) bond length labels
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.bondSpacing"><code>bondSpacing</code></a></td>
    <td>Double bond spacing
	in C-C bond length units:<br>
	<center>
	<em>spacing</em>*1.54 &Aring; = <em>spacing</em>*<em>scale</em> pixels
	</center>
	</td>
    <td align="CENTER"><code>0.18</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.chiralitySupport"><code>chiralitySupport</code></a></td>
    <td>When to show atom chirality (R/S).
	<ul>
	<li><code>off</code> - never</li>
	<li><code>selected</code> - if chiral flag is set for the molecule
	or the atom's enhanced stereo type is absolute
	</li>
	<li><code>all</code> - always</li>
	</ul>
	</td>
    <td align="CENTER"><code>off</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.colorScheme"><code>colorScheme</code></a></td>
    <td>Color scheme.
	<ul>
	<li><code>mono</code> - monochrome</li>
	<li><code>cpk</code> - Corey-Pauling-Kultun</li>
	<li><code>shapely</code> -
	    <a HREF="shapely-scheme.html">shapely</a> (residue types)</li>
	<li><code>group</code> - residue sequence numbers</li>
	</ul>
	</td>
    <td align="CENTER"><code>cpk</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.downWedge"><code>downWedge</code></a></td>
    <td>Wedge bond display convention.
	Down wedge points downward in MDL's convention (<code>mdl</code>),
	upward (at the chiral center) in Daylight's (<code>daylight</code>).
	</td>
    <td align="CENTER"><code>mdl</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.explicitH"><code>explicitH</code></a></td>
    <td>Show (true) or hide (false) explicit hydrogens
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.ezVisible"><code>ezVisible</code></a></td>
    <td>Show (true) or hide (false) E/Z labels
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.grinvVisible"><code>grinvVisible</code></a></td>
    <td>Show (true) or hide (false) graph invariants (canonical labels)
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.implicitH"><code>implicitH</code></a></td>
    <td>How to display H labels.
	<ul>
	<li><code>off</code></li>
	<li><code>hetero</code> - on heteroatoms</li>
	<li><code>heteroterm</code> - on hetero or terminal atoms</li>
	<li><code>all</code> - all atoms</li>
	</ul>
	</td>
    <td align="CENTER"><code>heteroterm</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.lonePairsVisible"><code>lonePairsVisible</code></a></td>
    <td>Show (true) or hide (false) lone pairs
	</td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.lonePairsAutoCalc"><code>lonePairsAutoCalc</code></a></td>
    <td>Switch on (true) or off (false) automatic calculation of lone pairs.
        The <a href="#parameters.lonePairsVisible">lonePairsVisible</a> parameter should
        be set to true to display the result of the automatic calculation.
        </td>
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.maxscale"><code>maxscale</code></a></td>
    <td>Maximizes the magnification for autoscale to prevent overscaling of small molecules.
	It is usually set to 28, which is the <a href="#parameters.scale">scale</a> factor for 100% magnification.</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.reactionErrorVisible"><code><strike>reactionErrorVisible</strike></code></a></td>
    <td>Deprecated.
    <td align="CENTER"><code>false</code></td></tr>
<tr valign="TOP"><td><a class="text" name="3d.rendering"><code>rendering</code></a></td>
    <td>Rendering style.
	<ul>
	<li><code>wireframe</code> - wireframe</li>
	<li><code>wireknobs</code> - wireframe with knobs</li>
	<li><code>sticks</code> - 3D sticks</li>
	<li><code>ballstick</code> - ball &amp; stick</li>
	<li><code>spacefill</code> - balls</li>
	</ul>
	</td>
    <td align="CENTER"><code>wireframe</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.rgroupsVisible"><code>rgroupsVisible</code></a></td>
    <td>Show (true) or hide (false) R-group definitions.
    </td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.scale"><code>scale</code></a></td>
    <td>Magnification.
	A 1.54 &Aring; long C-C bond is magnified to <em>scale</em> pixels.</td>
    <td align="CENTER"><code>28</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchAnyBond"><code>sketchAnyBond</code></a></td>
    <td>Display type of the Any bond in the sketcher:
    <ul>
        <li><code>auto</code> - displayed as dashed line in most cases, solid line only when
        all bonds are generated from atom coordinates (e.g. XYZ and PDB files).</li>
        <li><code>dashed</code> - displayed as dashed line</li>
        <li><code>solid</code> - displayed as solid line</li>
    </ul>
    </td>
    <td align="CENTER"><code>auto</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.stickdst"><code>stickdst</code></a></td>
    <td>Stick distance of atoms in C-C bond length units.</td>
    <td align="CENTER"><code>0.3</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.showSets"><code>showSets</code></a></td>
    <td>Show the specified atom sets only.
    Comma separated list of set sequence numbers (0, ..., 63).</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.showSketchCarbon"><code>sketchCarbonVisibility</code></a></td>
    <td>Display the label of carbon atoms in structures.
    <ul>
	<li><code>on</code> - Always show the atom labels of carbon atoms.</li>
	<li><code>off</code> - Never show the atom labels of carbon atoms.</li>
	<li><code>inChain</code> - Show the atom labels of carbon atoms at
	 straight angles and at implicit Hydrogens.</li>
	</ul>
    <td align="CENTER"><code>inChain</code></td></tr>      
<tr valign="TOP"><td><a class="text" name="3d.stickThickness"><code>stickThickness</code></a></td>
    <td>3D stick diameter for
	&quot;sticks&quot; and &quot;ballstick&quot;
	<a HREF="#3d.rendering">rendering modes</a>,
	in Angstroms.</td>
    <td align="CENTER"><code>0.1</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.valenceErrorVisible"><code>valenceErrorVisible</code></a></td>
    <td>Highlight (by underlining) the labels of
    those atoms with valence errors.
    This option can also be set on the
    <strong>Edit</strong>/<strong>Preferences</strong>/<strong>MarvinSketch</strong>
    panel.
	<ul>
	<li><code>true</code> - display errors</li>
	<li><code>false</code> - do not display errors</li>
	</ul>
	</td>
    <td align="CENTER"><code>true</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.viewAnyBond"><code>viewAnyBond</code></a></td>
    <td>Display type of the Any bond in the viewer:
    <ul>
    <li><code>auto</code> - displayed as dashed line in most cases, solid line only when
    all bonds are generated from atom coordinates (e.g. XYZ and PDB files).</li>
    <li><code>dashed</code> - displayed as dashed line</li>
    <li><code>solid</code> - displayed as solid line</li>
    </ul>
    </td>
    <td align="CENTER"><code>auto</code></td></tr>
<tr valign="TOP"><td><a class="text" name="3d.wireThickness"><code>wireThickness</code></a></td>
    <td>Line thickness for
	&quot;wireframe&quot; and &quot;wireknobs&quot;
	<a HREF="#3d.rendering">rendering modes</a>,
	in Angstroms.</td>
    <td align="CENTER"><code>0.064</code></td></tr>
</table>
</blockquote>

<h4><a class="anchor" name="structureparameters">1.1.3 &nbsp; Structure parameters</a></h4>
<blockquote>
<table BORDER=0 cellpadding="4" cellspacing="0" class="colored-grid" width="800">
<tr align="CENTER"><th width="20%">Parameter</th><th>Meaning</th><th width="10%">Default</th></tr>
<tr valign="TOP"><td><a class="text" name="parameters.atomSetColor"><code>atomSetColor0<br>atomSetColor1<br>...<br>atomSetColor63</code></a></td>
    <td>Atom set color as hexadecimal value.</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.bondSetColor"><code>bondSetColor1<br>...<br>bondSetColor63</code></a></td>
    <td>Bond set color as hexadecimal value.</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.importConv"><code>importConv</code></a></td>
    <td>Conversion(s) after molecule
	loading. Currently the following options are implemented:
	<table CELLSPACING=0 CELLPADDING=3 border="0" id="no-grid">
	<tr><td NOWRAP>&quot;a&quot; or &quot;+a&quot;&nbsp;&nbsp;&nbsp;&nbsp;</td>
	    <td><a href="../sci/aromatization-doc.html#daylight_arom">General</a> aromatization </td></tr>
    	<tr><td NOWRAP>&quot;a_bas&quot; or &quot;+a_bas&quot;&nbsp;&nbsp;&nbsp;&nbsp;</td>
	    <td><a href="../sci/aromatization-doc.html#basic">Basic</a> aromatization </td></tr>
	<tr><td NOWRAP>&quot;-a&quot;</td>
	    <td>dearomatization</td></tr>
	<tr valign="TOP"><td NOWRAP>&quot;H&quot; or &quot;+H&quot;&nbsp;&nbsp;&nbsp;&nbsp;</td>
	    <td>add explicit H atoms</td></tr>
	<tr valign="TOP"><td NOWRAP>&quot;-H&quot;</td>
	    <td>remove explicit H atoms</td></tr>
	 <tr valign="TOP"><td NOWRAP>&quot;c&quot;</td>
	    <td>automatic cleaning</td></tr>
	</table></td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.cleanDim"><code>cleanDim</code></a></td>
    <td>Number of space dimensions for cleaning.
	<ul>
	<li><code>2</code> - two-dimensional cleaning</li>
	<li><code>3</code> - three-dimensional cleaning</li>
	</ul>
	See also: <a href="#parameters.cleanOpts">cleanOpts</a>,
		  <a href="#parameters.importConv">importConv</a>.</td>
    <td align="CENTER"><code>2</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.cleanOpts"><code>cleanOpts</code></a></td>
    <td>Options for 2D or 3D cleaning.<br>
        <code>cleanOpts</code> accepts the same parameter values as
        <a href="#parameters.clean2dOpts">clean2dOpts</a> or
        <a href="#parameters.clean3dOpts">clean3dOpts</a>
	depending on the cleaning dimension
        (<a HREF="#parameters.cleanDim">cleanDim</a>).
        </td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.clean2dOpts"><code>clean2dOpts</code></a></td>
    <td>Options for 2D cleaning (0D-&gt;2D)
	See <a href="../sci/cleanoptions.html#base.2d">base 2D cleaning
        options</a>
	</td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.clean3dOpts"><code>clean3dOpts</code></a></td>
    <td>Options for 3D cleaning (0D-&gt;3D)
	See <a href="../sci/cleanoptions.html#base.3d">base 3D cleaning
        options</a>
	</td>
<td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.setColoringEnabled"><code>setColoringEnabled</code></a></td>
    <td>Atom/bond set coloring.</td>
    <td align="CENTER"><code>true</code></td></tr>
</table>
</blockquote>

<h4><a class="anchor" name="otherparameters">1.1.4 &nbsp; Other parameters</a></h4>
<blockquote>
<table BORDER=0 cellpadding="4" cellspacing="0" class="colored-grid" width="800">
<tr align="CENTER"><th width="20%">Parameter</th><th>Meaning</th><th width="10%">Default</th></tr>
<tr valign="TOP"><td><a class="text" name="parameters.escapeChar"><code>escapeChar</code></a></td>
    <td>Escape character to use for parsing the value of the
	<a href="#parameters.mol">mol</a> parameter.</td>
    <td align="center">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.abbrevgroups"><code>abbrevgroups</code></a></td>
    <td>Location of the file containing
	the abbreviated groups.</td>
    <td align="LEFT"><code>chemaxon/marvin<br>
			 /templates<br>
			 /default.abbrevgroup</code></td>
    </tr>
<tr valign="TOP"><td><a class="text" name="parameters.copyAsFormat"><code>copyAsFormat</code></a></td>
    <td>Default clipboard format by Copy As action.</td>
    <td align="center">platform dependent</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.copyOpts"><code>copyOpts</code></a></td>
    <td>Deprecated. Since 5.3 it has no sense. It will be deleted in 5.4.</td>
    <td align="CENTER">platform dependent</td></tr>
<tr VALIGN=TOP><td><a class="text" name="parameters.defaultSaveFormat"><code>defaultSaveFormat</code></a></td>
    <td>Sets the default chemical file format in the Save As dialog.
    </td>
    <td ALIGN=CENTER><code>mrv</code></td></tr>
<tr valign="TOP"><td><code>debug</code></td>
    <td>Debug mode. Possible values: 0, 1, 2.</td>
    <td align="CENTER"><code>0</code></td></tr>
<tr VALIGN=TOP><td><a class="text" name="parameters.menuconfig"><code>menuconfig</code></a></td>
    <td>Specifies an alternative menu customization file location instead of the default
    <code>.chemaxon/{MarvinSketch_version}/customization.xml</code> (Unix) or
    <code>chemaxon/{MarvinSketch_version}/customziation.xml</code> (Windows) file under the user's home.
    Please note that if this parameter is used, the <a HREF="#parameters.customizationEnabled">customizationEnabled</a>
    parameter is automatically set to false.
    </td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.mergedst"><code>mergedst</code></a></td>
    <td>Merge distance of atoms in C-C bond length units.</td>
    <td align="CENTER"><code>0.1</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.molFormat"><code>molFormat</code></a></td>
    <td>Default file format:
	<code>mol</code>, <code>csmol</code>,
	<code>smiles</code>, <code>cxsmiles</code>,
	<code>cml</code>, <code>pdb</code>, <code>pov</code>, <code>sybyl</code>,
	or <code>xyz</code>.</td>
    <td align="CENTER"><code>mol</code></td></tr>
<tr VALIGN=TOP><td><a class="text" name="parameters.shortcuts"><code>shortcuts</code></a></td>
    <td>Specifies an alternative shortcut customization file location instead of the default
    <code>.chemaxon/{MarvinSketch_version}/shortcuts.xml</code> (Unix) or
    <code>chemaxon/{MarvinSketch_version}/shortcuts.xml</code> (Windows) file under the user's home.
    Please note that if this parameter is used, the <a HREF="#parameters.customizationEnabled">customizationEnabled</a>
    parameter is defaults to false.
    </td>
    <td align="CENTER">&nbsp;</td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchHelp"><a class="text" name="sketchHelp"><code>sketchHelp</code></a></a></td>
    <td>MarvinSketch help contents.</td>
    <td align="LEFT"><code>chemaxon/marvin/help<br>
		/sketch-index.html</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.sketchQuickHelp"><a class="text" name="sketchQuickHelp"><code>sketchQuickHelp</code></a></a></td>
    <td>MarvinSketch quick help.</td>
    <td align="LEFT"><code>chemaxon/marvin/help<br>
		/sketch.html</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.undo"><code>undo</code></a></td>
    <td>Maximum number of undo operations.</td>
    <td align="CENTER"><code>50</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.viewHelp"><a class="text" name="viewHelp"><code>viewHelp</code></a></a></td>
    <td>MarvinView help contents.</td>
    <td align="LEFT"><code>chemaxon/marvin/help<br>
		/view-index.html</code></td></tr>
<tr valign="TOP"><td><a class="text" name="parameters.viewQuickHelp"><a class="text" name="viewQuickHelp"><code>viewQuickHelp</code></a></a></td>
    <td>MarvinView quick help.</td>
    <td align="LEFT"><code>chemaxon/marvin/help<br>
		/view.html</code></td></tr>
</table>
</blockquote>


<p><!--APPLETONLY_BEGIN-->
Applet example:
<blockquote><pre>
&lt;applet CODE=MSketch WIDTH=480 HEIGHT=400&gt;
&lt;param NAME=&quot;background&quot; VALUE=&quot;#cccccc&gt;
&lt;param NAME=&quot;molbg&quot; VALUE=&quot;#ffffff&quot;&gt;
&lt;param NAME=&quot;implicitH&quot; VALUE=&quot;hetero&quot;&gt;
&lt;/applet&gt;
</pre></blockquote>
<!--APPLETONLY_END-->

<!--APPLETONLY_BEGIN-->
<h3><a class="anchor" name="appletonly">1.1 &nbsp; Applet only parameters</a></h3>

The following parameters are meaningful only for the applets (MSketch,
JMSketch) and not for the JavaBean (MSketchPane).
<p>

<blockquote>
<table BORDER=0 cellpadding="4" cellspacing="0" class="colored-grid">
<tr align="CENTER"><th>Parameter</th><th>Meaning</th><th>Default</th></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.menubar"><code>menubar</code></a></td>
    <td>Enable the embedded menubar.</td>
    <td align="CENTER"><code>true</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.buttonmenubar"><code>buttonmenubar</code></a></td>
    <td>Enable menubar in button (/hide) mode if
    the <a href="#parameters.menubar">menubar</a> parameter is <code>true</code>.
    Combine it with the <a href="#parameters.detach">detach</a> parameter to
    set the button mode.<br>
    <code>True</code>, to allow, <code>false</code> to deny menu bar on the big sketcher
    button.</td>
    <td align="CENTER"><code>true</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.detach"><code>detach</code></a></td>
    <td>Detachment behavior.
    	The value consists of some optional arguments: <code>show/hide</code>
	<code>size</code>, and <code>maxscale</code>. If more arguments are included, they must
	be separated by a comma.<BR>
	To detach the sketcher from the web page and display it in a separate window,
	set <code>&quot;show&quot;</code>.<BR>
	To detach the sketcher without displaying the separate window,
	set <code>&quot;hide&quot;</code>.<BR>
	Both settings make the applet on the web page look like a molecule
	viewer.<br><BR>
	The initial size of the sketcher window can be specified with
	&quot;<code>size=</code><em>width</em><code>x</code><em>height</em>&quot;
	<BR>Examples: &quot;<code>show</code>&quot;,
	&quot;<code>size=500x500</code>&quot;,
	&quot;<code>hide,size=500x500</code>&quot;.<br>
        In case the <code>maxscale</code> argument is set, it can prevent small molecules
        to be overscaled on the button.<br>
        Example for maximum 100% magnification: &quot;<code>hide,maxscale=28</code>&quot;<br>
        Live applet example: <a href="../../examples/applets/sketch/detach.html">MarvinSketch Example - Pure visualization mode</a>
        </td>
    <td align="CENTER"><code>size=444x350</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.undetachByX"><code>undetachByX</code></a></td>
    <td>Sketcher window close (x)
	behavior.<br>
	<code>false</code>: always hide sketcher<br>
	<code>true</code>: replace viewer component by sketcher in web
	browser window if the applet is large enough (&gt;= 400x300)
	</td>
    <td align="CENTER"><code>true</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.mol"><code>mol</code></a></td>
    <td>The molecule file to be loaded at startup,
    	as either a URL
	or the file itself (inline) in MDL mol, compressed mol, SMILES,
	SMARTS, etc format.<br>
	Newlines occurring in the string must be replaced or preceded by "\n"
	and backslashes are recommended to be escaped as "\\".<br>
	The file format and/or import options can be specified if one
	of the following forms is used:<br>
	&quot;file{options}&quot;,<br>
	&quot;file{MULTISET,options}&quot;,<br>
	&quot;file{format:}&quot;,<br>
	&quot;file{format:options}&quot;, or<br>
	&quot;file{format:MULTISET,options}&quot;.<br>
	If the MULTISET option is specified, then a multi-molecule file is
	read into one molecule object containing multiple atom sets.<br>
	Examples: "foo.xyz{f1.4C4}",
	"foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"
	</td>
    <td>&nbsp;</td></tr>
  <tr valign="TOP"><td><code><strike>preload</strike></code></td>
    <td>Deprecated
	</td>
    <td align="CENTER">&nbsp;</td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.cacheMols"><code>cacheMols</code></a></td>
    <td>Store loaded molecules in an internal
	cache (<code>true</code> or <code>false</code>).
	</td>
    <td align="CENTER"><code>false</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.loadMols"><code>loadMols</code></a></td>
    <td>Comma-separated list of molfiles to
	preload.
	Useful for caching molecules in JavaScript &quot;slideshows&quot;.
	</td>
    <td align="CENTER">&nbsp;</td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.usedJars"><code>usedJars</code></a></td>
    <td>Comma-separated list of additional
	jar files that can be used by the applet. The additional
	files have to be defined with their paths relative to the applet's base.
	</td>
    <td align="CENTER">&nbsp;</td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.imageSaveURL"><code>imageSaveURL</code></a></td>
    <td>The URL of the cgi, jsp or asp
	file use to save the image posted by the applet to the server.<br>
	The cgi has to read the image from the standard input into a byte
	array, save it to a temporary file and send back the absolute path
	of the file to the applet.<br>
	A jsp example: <a href="../../sketch/saveimage_jsp.txt"><code>saveimage.jsp
	</code></a>
        </td>
    <td>&nbsp;</td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.imageSaveFormat"><code>imageSaveFormat</code></a></td>
    <td>The default file format for
	image saving.
        </td>
    <td align="CENTER"><code>png</code></td></tr>
  <tr valign="TOP"><td><a class="text" name="parameters.imageShowURL"><code>imageShowURL</code></a></td>
    <td>The URL of the cgi, jsp or asp
	file that either saves the data into a file generated by the applet
	or shows the generated image that  was saved to a temporary file by
	<code>imageSaveURL</code>.<br>
	The posted parameters:
	<blockquote>
	<table BORDER=0 cellpadding="4" cellspacing="0" id="no-grid">
	<tr><th>name</th><th>description</th>
	    </tr>
 	<tr><td><code>filename</code></td>
	    <td>If the applet generated an image, it was saved into a temporary
		file on the server. In this case this parameter contains the
		absolute path of the temporary file.</td></tr>
 	<tr><td><code>type</code></td>
	    <td>Sets the type of the file and its extension. <br>
		 It can be:<code> "mol", "csmol", "pdb", "sybyl", "xyz", "jpeg",
		"png", "pov", "svg"</code>.</td></tr>
	<tr><td><code>where</code></td>
	    <td>Sets the location in which the image will be "shown"<br>
		Possible values:<code> "file", "browser", null</code>. <br>
		<ul>
			<li>"file" - the generated data will be saved into a file.
			<li>"browser" - the data will be displayed in a browser window.
		</ul>
		</td></tr>
	<tr><td><code>data</code></td>
	    <td>If the applet generated a kind of molecule format file (see:
		<a href="../formats/formats.html">formats</a>), it is posted by this
                parameter. In this case the text file have to be saved as a
                file.</td></tr>
	</table>
	</blockquote>
	A jsp example: <a href="../../sketch/showimage_jsp.txt"><code>showimage.jsp
	</code></a></td>
    <td>&nbsp;</td></tr>
    <tr valign="TOP"><td><a class="text" name="parameters.molLoaderFinishedEvent"><code>molLoaderFinishedEvent</code></a></td>
    <td>Evaluates a JavaScript code after
     the loading of the molecule into the editor is finished.
     This <i>"event"</i> is invoked if molecule is loaded-in into the applet
     in any of the following cases:
     <ul>
        <li>Automaticaly, at applet starting: (using the
            <a href="#parameters.mol">mol</a> applet parameter)</li>
        <li>Calling <i>(J)MSketch.setMol(...)</i> from JavaScript.</li>
     </ul>
     Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet.
     E.g.:<pre>
     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("mol","caffeine.mol");
     msketch_param("molLoaderFinishedEvent","js:alert('Molecule is loaded-in.')");
     msketch_end();
     </pre>
    </td>
    <td>&nbsp;</td></tr>
    <tr valign="TOP"><td><a class="text" name="parameters.listenpropertychange"><code>listenpropertychange</code></a></td>
    <td>Switch on/off property
    change event listener to the applet. If listener is active, the applet will
    call <strong>propertyChange(prop)</strong> JavaScript method.
    If you would like to handle property change events in JavaScript, implement
    this method in your html source.
     Note: If the MAYSCRIPT option is not specified, JavaScript can not be evaluated from the applet.
     E.g.:<pre>
     function propertyChange(prop) {
        if(document.textform != null) {
            var s = document.textform.txt.value;
            document.textform.txt.value = s + "\n" + prop;
        }
     }

     msketch_mayscript=true;
     msketch_begin("marvin",400,300);
     msketch_param("listenpropertychange","true");
     msketch_end();
     </pre>
     If you also specify the "appletid" parameter, its value will appear in 
     the name of the property as prefix (e.g.: "firstapplet.mol").
    </td>
    <td><code>false</code></td></tr>
<tr valign="TOP"><td><code><a NAME="parameters.appletid" 
        class="text">appletid</a></code></td>
    <td>Identify applet in property change event notifications to JavaScript.
    Use this parameter with <a href="#parameters.listenpropertychange">listenpropertychange</a>
    when more than one applet are located on the same web page. It helps
    to identify which applet sent the notification.</td><td></td></tr>
    <tr valign="TOP"><td><a class="text" name="parameters.skin"><a class="text" name="skin"><code>skin</code></a></a></td>
    <td>Change the component's Look & Feel (only in SWING applet).
    	If you do not specify this parameter,
	Marvin will use the default LookAndFeel style.
	<BR>This parameter value is the name of the new LookAndFeel class.
	</td>
    <td align="LEFT"><code>javax.swing.plaf<br>
		    .metal<br>
		    .MetalLookAndFeel</code></td></tr>
	<tr VALIGN=TOP><td><a NAME="parameters.splashScreenImage" class="text"><a class="text" name="splashScreenImage"><code>splashScreenImage</code></a></a></td>
    <td>Change the component's splash screen displayed at startup.
    	If you do not specify this parameter, Marvin will use its default splash screen.
	<BR>This parameter value is the relative path of the image, specify relatively to the CODEBASE<br>
	<font style="font-size: 10px;">Note: Animated gif files can be displayed badly (flashing, or too fast animation)</font>
	</td>
    <td ALIGN=LEFT><code>null</code></td></tr>

    <tr VALIGN=TOP><td><a NAME="parameters.license" class="text"><a class="text" name="license"><code>license</code></a></a></td>
    <td>Sets the contents of a pre-read license file to the license manager to read and validate licenses from.
    </td>
    <td>&nbsp;</td></tr>
    <tr VALIGN=TOP><td><a NAME="parameters.licenseFile" class="text"><a class="text" name="licenseFile"><code>licenseFile</code></a></a></td>
    <td>Sets the license file location to the license manager to read and validate licenses from.
    </td>
    <td>&nbsp;</td></tr>
    <tr VALIGN=TOP><td><a NAME="parameters.legacy_lifecycle" class="text"><a class="text" name="legacy_lifecycle"><code>legacy_lifecycle</code></a></a></td>
    <td>The "legacy_lifecycle" is a general Java applet parameter. If its value
    is true, it
    helps avoid destroying the applet when you leaves the applet page.
    If you use "marvin.js", it sets its value to true automatically unless you specify its value explicitly. By the way, the default value of this parameter in Java
    is false.
    See the discussion about it on the 
    <a href="http://www.chemaxon.com/forum/ftopic4945.html">forum</a>.</td>
    <td>&nbsp;</td></tr>
</table>
</blockquote>
<!--APPLETONLY_END-->
<p>

</body>
</html>
